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Buffer illustrates what?
The law of mass action: Add reactants speed reaction as well decrease product increase reaction
Titration curve of weak acid base
Gives the protonation state and reactivity at given pH
Are made the same wayt in all living things and are present in all organismn in roughly the same proportions
Condensation Reaction (polymerization)
- Releases a molecule of water for each covalent bond formed.
- Anabolic Reaction
Hydrolysis Reaction (Depolymerization)
- Consumes a molecule of water for each covalent bond broken.
- Catabolic Reaction
Molecule has same chemical formula, but different arrangment of atoms.
Isomer, where the group is attached to a different carbon atom
CH3-CHOH-CH3 and CH3-CH2-CH2-OH are what and why?
They are structural isomer groups because the "group" in this case OH group is attached to a different carbon atom
A group is attached in different ways to the carbon atom...are mirror images of each other.
When do Optical Isomers occur
When a carbon has 4 different atoms of groups attached to it.
What is this? and why?
Optical isomer, because it is a mirror image and there are 4 carbons.
Function of Carbohydrates?
- * Act as energy storage and building blocks for other molecules (nucleic acids)
- * structural component (wood)
- * Attach to many membrane proteins and lipids and sometimes provided identity to cells (human blood group)
3 major categories of Carbohydrates?
General formula for carbohydrate monomer?
Multiples of CH2O...1 carboxyl group, several hydroxyl groups. (ie C6H12O6)
Why are polymers slightly different then monomers?
Because water is lost during condensation
In solution, glucose exist...
As a staight chain and as a ring. The ring form is predominant.
What are the two forms of ring of glucose in solution?
- alpha- glucose and beta-glucose.
- They exist in equilibrium
2-OH is trans H2OH
Beta - glucose
2-OH is cis H2OH
- straight chain
- alpha (1-->4) link
- ALWAYS straight chain
- Beta (1-->4) link
- alpha (1-->4) link
Examples of starch
- Amylose- Unbranched
- Amylopectin- moderately branched (plants)
- Glycogen -highly branched (animals)
- Beta (1-->4) link
- Always unbranched
What is this? and explain
- (1-4) alpha link
- Sometimes branched
what is this?
- Beta (1-->4) link
- Always straight
Is starch branched
- in Amylase its unbranched
- Amylopectin its moderately branched
- Glycogen its highly branched
Contains information to make your genes
DNA is trancribed...into
RNA which is translated into proteins
Whats is another function of nucleotides
Have additional functions as signaling molecules and energy transducers
Subunit of nucleic acid is?
Sugar is in which position
(5' to 3' position)
Nucleiotide consist of?
Phosphate, sugar, base
Nucleic Bases are?
- (T is replaced by U in RNA)
- pyrimidine with purine
In what direction does polymerization occur?
- 5' to 3' direction
- Successive nucleiotides add the 3' end of the polymer
What is the 5-3link called?
DNA vs. RNA
- Double Stranded
- sugar: deoxyribose
- Bases: A,C,G, Thymine
- Single Stranded
- sugar: ribose
- A,C,G, Uracil
- Double ring
- single ring
Orientation of DNA
- 5-->3down, 3--> up
- Antiparallel orientation
- minor or major groves
- Single C-C bonds (saturated with hydrogen)
- Form part of animal fat
- Solid at room temperature
- At least 1 C=C double bond (not completely saturated)
- Form part of plant oil
- Liquid at room temperature
Why are lipids insoluble in water?
Many non polar covalent bonds of hydrogen and carbon
Roles of lipids
- Energy storage
- Cell membrane
- Capture of light energy
- Hormone and vitamins
- Thermal insulation
- Water repellency
- Electrical insulation of nerves
Glycerol + 3fatty acid molecules = 3H2O+ Triglyceride (esterlinkage)
Phospholipids have two hydrophobic fatty acids (tails)and one hydrophilic headgroup attached to glycerol
How do phospholipids assemble?
They self assemble into a bilayer because of hydrogen bonding and hydrophobic interactions
What are proteins?
Polymers of amino acids
What is crutial to proteins
Folding is crutial to the function of the protein and is influenced largely by the sequence of amino acids
- Precise sequence of amino acids...
- Peptide backbone that consist of repeating units of atoms:
Draw Bondimg of Peptide linkage
All 20 amino acids have which structure and when?
at cytoplasmic pH!
Types of Amino Acids?
- Electrically charged hydrophilic side chains
- Polar but uncharged side chains
- O or OH
- Nonpolar hydrophobic side chains
What are two common secondary structures of proteins?
αhelix and the β pleated sheet.
A protein’s secondary structure consist of?
- Regular, repeated patterns in different regions inthe polypeptide chain
- • This shape is determined primarily by hydrogen bonds between amino acids.
Forms straight rod
The H-bonds (N-H----O=C)are formed by thebackbone and are parallelto the axis of the helix.
- The side groups (Rgroups) of the amino acids project outward (away)from the helix.
- coiled coils
When do coiled coils arise?
- When two α helixes have hydrophobic amino acids at every 4th position
- * think keratins in hair and feathers.
Why can alpha helixes be inserted in the plasma membrane?
Because all the H-bonds run parallel to the helix axis. This is if the helix only contains hydrophobic amino acids side chains
β pleated sheet?
- Makes flat plates (R group project up and down from the sheet)
- strands can run anti parallel or in parallel direction
Fits neither in a αhelix nor in a β sheet,because it makes a kink inthe peptide, and because theN carries no H for hydrogenbonding
Three-dimensional shape ofthe completely foldedpolypeptide
The structure of multiplepolypeptides forming aprotein complex
Tertiary structure is determined by:
- location of disulfide bridges
- location of secondary structures
- ionic interactions between positive andnegative charges deep in the protein, awayfrom water
- Hydrophobic aggregation of R groupsstabilized by van der Waals forces (important non covalent interaction)
Denaturation of proteins?
The loss of a proteins Norman 3D structure and function
- Occurs in test tube
- Shows that proteins automatically fold into a conformation of lowest energy
- All folding information is contained within theprimary sequence
What can cause denaturation?
- Changes in temperature or pH
- Examples: cooking,fever, lemon juice in milk
Can denatured proteins be refolded?
No, it is degraded by the proteasome
What is constanly happening in the cell
Protein turnover (breakdown and resynthesis)
What are chaperones?
Are specialized proteins that helpkeep other proteins (temporarily exposedhydrophobic regions) from interactinginappropriately with one another
- They do so by sequestering some newlysynthesized proteins to give them time to fold
Role of phospholipid bilayer?
Seperate two aqueous regions
Role of cholesterol in the phospholip bilayer?
Cholesterol has a rigid ring structure which makes the membrane more solid (counteractes the effect of unsaturated fatty acid)
What is favorable for the bilayer
It is energically favorable for the bilayer to seal/form an enclosed space.
The two dimentional fluid has four types of movement?
- Lateral diffusion
- Flexion (swaying)
- Flip flop (leaflet changes spot..rare)
What kind of symmetry is the phospholid bilayer?
How do proteins insert into the membrane?
By exposing hydrophobic amino acids in transmembrane area.
- Have hydrophobic regions of aminoo acids that cross the phospholipid bilayer.
- They have a specific orientation, showing different "faces on the two sides of the membrane.
Peripheral membrane proteins?
Lack hydrophobic regoins and are not embedded in the bilayer. They are covalently attached to lipids or bind noncovalently to other transmembrane proteins
What is diffusion
The passive mixing of substances resulting in transport along a concentration gradient
In what motion does diffusion happen in?
It happends in brownian motion- Random motion
What is the diffusion rate determined by?
- Size of molecule
- Concentration Gradient
What can cross the membrane?
water, gasses, hydrophobic molecules
What can sometimes cross the membrane?
Small uncharged polar molecules
What can't cross the membrane?
Large polar molecules and ions
What is osmosis?
Diffusion of water across a selectively permeable membrane.
In what direction does water move in?
Water moves from a low solute concentration to regions of high solute concentration
High solute concentration compared to cell
Concentration of solute is the same in the cell and the outside
Concentration of solute is greater in the cell than it is on the outside.
Passive Diffusion: Facillitated diffusion?
Because large polar and charged substances do not diffuse across the lipid bilayer...facillitated diffusion allows these important materials to enter the cell
Ion channels - can be openned or closed on a signal
- Bind to the substance (example glucose) and release it in the cell.
- It can also be reversed, so if there is too much inside it will do the reverse.
What happends when all the binding sites are occupied?
The carrier protein becomes saturated; therefore the rate of diffusion levels off
Difference between diffusion and active transport?
Active transport requires expenditure of energy (provided by ATP)
Substances are moved across the membrane against the concentration gradient
Primary active Transport, explain?
Secondary Active Transport
- use established gradients to move substanceso
- uses ATP indirectly. The ATP molecules are consumed to establish the ion gradiento
- the gradient is then used to move a substance as described for the symport and antiport system
- uses energy from ions moving down the concentration gradient to drive the movement of other ions (ie Na+ helps sugar)
- both movements are in the same directio
- Similar, but opposite. uses energy from ions moving down the concentration gradient to drive the movement of other ions in the opposite direction
- eg glucose can enter a cell via facilitated diffusion or via symport with Na+, with help from the NaK pump
- example: gut. Moves glucose into cell from gut via symport with Na+, powered by NaK pump, moves glucose into blood via diffusion
Why is glucose not transported in the cell by just using ATP?
- Its more economical to use sodium gradient
- It also creates more flexibility for the cell to transpot thing with the gradient
Why are cells so small?
- Facilitates diffusion (chemical processes)
- Diffusion happends much easier with a large surface area (high surface area to volume ratio)
- Cells with no nucleus
- Very small
- Cell with a membrane enclosed nucleus
- Thats why they can be bigger than prokaryotes
What can prokaryotes digest?
Anything!! Large metabolic diversity
Where is DNA found in prokaryotes
In the nucleoid, its single stranded
What essential to eukaryotes?
Compartmentazation: each organelle or compartment has a specific role defined by chemical proccesses
Role of Plasmodesmata?
What do vacuoles do?
Stores water that keeps the cell rigid
Cell wall is made out of?
Explain the Endomembrane system?
- All of the membranes in the cells are related
- Vesicles can pinch off nuclear membranes to ER to Golgi to cell membrane and back
- Orientation of membrane is always preserve
What happends in the nucleolus?
Ribosomes are assembled from RNA and protein
What happends in the Nucleus?
- DNA is replicate
- DNA is transcribed into mRNA (messenger RNA) or rRNA (ribosome) by RNA polymerases
- rRNA is not translated; it directly folds into a 3D structure
- Ribosomes are made of 4 rRNAs and about 80 proteins in the nucleolus (RNAs largely determine structure and function
What is the nucleolus?
The round granular structure within the nucleus of a cell, and composed of protein and RNA
What forms the nuclear envelope?
Two lipid bilayers surround nucleus. Perforated with nuclear pore
What do ribosomes do?
Translate mRNA into protein only in the cytoplasm and feed it to the ER.
Where do you find functional ribosomes?
Are find free in the cytoplasm, mitochondria, bound to the endoplasmic reticulum, and in chloroplasts.
What is the endoplasmic reticulum?
A network of interconnecting membranes distributed throughout the cytoplasm
What is the internal part of the ER?
The internal compartment, called the lumen, is a separate part of the cell with a distinct protein and ion composition. It communicates only with the outside of the cell
What does the folding of the ER generate?
A surface area much greater than that of the plasma membrane
What happends at certain cites of the ER?
The ER membrane is continuous with the outer nuclear envelope membrane
Rough Endoplasmic Reticulum?
- Has ribosomes attachd to it.
- These come from the cytosolic pool of ribosome’s and are directed to the ER after they have translated the first few amino acids containing a signal sequence that directs the ribosomes to the ER
- sugars (oligosaccharides 3-12 subunit sugars) are added to proteins her
Smooth Endoplasmic Reticulum?
Where are lipids synthesized?
In the ER, make them water soluble and can be excreted in the urine. Enzymes in the ER also detoxify many substances.
- Receive proteins from the ER and further modify them (especially oligosaccharides) Add oligosaccharides to membrane lipids
- Concentrate, package and sort proteins before they are sent to their destination (apical or basal side of plasma membrane, lysosome)
What are lysosomes?
- Are vesicles containing digestive enzymes that come in part from the Golgi
- Are sites for breakdown of food and foreign material brought into the cell by phagocytosis (cell eating)
- The site where digestion of spent cellular components occurs
- Can eat their host cell (autophagy), either regulated (leaves in fall), or due to nutrition deprivation
What is exocytosis?
Cell directs the contents (waste products, digestive enzymes, milk) of secretory vesicles out of the cell membrane
What is endocytosis?
Food is brought into the cell and digested, often receptor mediated
What is the Endosymbiont theory and what is the evidence?
Mitochondria and chloroplasts are descendants of bacteria
- double membrane (likely taken up by endocytosis) Own genome
- Own ribosomes more similar to Eubacteria
- Genes more similar to Eubacteria
However, there is no vesicle exchange between mitochondria/choloroplasts and the endomembrane system
What is the cytoskeleton?
- Maintains cell shape and polarity
- Provides the mechanisms for cell movment
- Acts as tracks for “motor proteins” that help move materials within the cell
What are Intermediate filaments and what do they do?
- Are found only in multicellular organisms, forming rope like assemblages in cells
- Have only structural functions:
- To stabilize the nucleus (lamins)
- To give mechanical strength to cells (coiled coils of keratin)
What are Microtubules? What do they do?
Microtubules are hollow cylinders made from tubulin protein structures.
Organize the cell
How does the micromolecule organise the cell?
- Provide an intracellular skeleton
- Determine cell polarity
- tracks wheremotor proteins can move vesicles and organelles (also move chromosomes)
How can micromolecules move?
- They can move in both direction by the motors dyein and kinesin that walk in opposite directions
- "can be moved like cargo"
Locomotive appendage made out of micromolecules
- Locomotive appendage made out of micromolecules
- It is the doublets of MT, connected by dyen
What are the 5 major types of cell junctions?
- Tight Junction
- Adherens junction
- Gap junctions
- Focal Adhesion
What do proteins do for actin
They regulate the growth or shrinkage of micotubules
- Separates apical(outside) and basolateral(inside) membrane domains and their membrane proteins
- Prevents substances from moving through the intercellular space
- The adherens junction is the most important and ancient cell-cell junction
- first one toform during development.
- Generally form a circumferential belt close to theapical-basolateral boundary
- • Adherens junctions are made of transmembrane cadherins. Several cadherins from two different cells bind to each other
- • Adherens junctions connect to actin filaments.
Provide mechanical strenght (skin) are connected to intermediate filaments
Connections that facilitatecommunication between cells. Low molecularweightmolecules can freely diffuse from one cellto the next (e.g. Ca2+ ion to synchronize heartmuscle contraction).
Made of proteins called connexins, which snap together to generate a pore.
- Most important cell matrix junction
- Form distinct spots on the basal side of cells. They connect skin to the underlying basal lamina, muscles to tendons, ….
- made of transmembrane integrins
- connect to actin filaments
cells must constantly aquire________from their enviroment?
Reactions link simple molecules togetherto make complex ones. These are energy-storingreactions. They require energy.
Reactions break down complexmolecules into simpler ones. They release energy.
Potential Energy due to position---->Kinetic Energy---->Heat Energy
First Law of Thermodynamics?
During anyconversion of energy, the total initial energy equals the total final energy. Energy is neither created nor destroyed
Second Law of Thermodynamics?
Energy spontaneously dispersesfrom being localized to becoming spread out if it is not hinderedfrom doing so (entropy increases)
Energy conversions, e.g. chemical reactions only occur if energydisperses in the universe. The dispersing energy is the drivingforce for energy conversions.
How can a cell release free energy (drive a chemical reaction)?
By dispersing energy/increasing entropy
How can a cell release free energy (drive a chemical reaction)?By dispersing energy/increasing entropy. How?
- 1) with a chemical reaction creating disorder in the cell(digesting a polymer)
- 2) with a chemical reaction releasing heat whichgenerates disorder/disperses energyin the surrounding (environment)
If ΔG is negative?
energy is released/dispersed(disorder is created)
If ΔG is positive?
energy is required
Four types of reactions (ΔG = ΔH - TΔS)?
1) heat is released and disorder is increased:always spontaneous (exergonic)
2) heat is released, but disorder decreases: onlyspontaneous below a certain temperature; e.g.denatured/native protein, lipid bilayer vs.individual lipidsThis reaction occurs only (-ΔG) if the heat releasedis greater than the increase in order.
3) heat is used, but disorder increases:spontaneous above a certain temperature; e.g.dissolving NaCl in water.
4) heat is used and disorder decreases: neverspontaneous (endergonic).Most anabolic reactions!
How do endergonic (anabolic) reactions occur?
By coupling endergonic to exergonic reactions!
More complications of thermodynamics?
- • In principle, all reactions are reversible (A--- B)
- • Adding more A speeds up the forward reaction,adding more B speeds up the reverse reaction.
- • At the point of chemical equilibrium, the relativeconcentrations of A and B are such that forward and reverse reactions take place at the same rate(ΔG = 0).
the___________have to be taken into account in most cases to calculate the actual ΔG.
All living cells use ___________for capture, transfer, and storage of energy
adenosine triphosphate (ATP)
ATP + H2O ADP + Pi + free energy
Why is the P-O bond higher than the H-O bond that forms after hydrolysis?
Phosphates are negatively charged, so energy is required to get them near each other to bond
• ADP is constantly removed either by reforming ATPor by hydrolysis to AMP (ΔG° = -7.3kcal/mole)
Why is ATP useful as the energy currency?
ΔG is intermediate between what you gainin respiration and what you expend in anabolism
Overall ΔG of coupled reactions must be_________ to proceed!!
Exergonic reactions proceed only after the addition of a small amount of energy, the__________
substance that speeds up a chemical reaction without being consumed (lowers Ea)
Most biological catalysts are proteins called?
Enzymes bind specific reactant molecules called?
Substrates bind to a particular site on the enzyme surface called the _______ where catalysis takes place
Enzymes catalyze reactions by using one or more of?
- Orientation substrates
- Inducing strain in the substrates
- Adding charges to substrate
Some enzymes require _______ in order to function
- These can be metal ions (zinc, copper), small org molecules temporarily binding, and small org molecules that are permanently bound to the protein (heme)
- Can become saturated if all ful
Only reactions with overall -ΔG or +ΔG can be catalyzed?
Regulates the whole pathway
What does multiple feeback control allows the cell to do?
adjust the ratio ofdifferent compounds (e.g.amino acids)
- • Enzyme activity can be inhibited by natural andartificial binders
- • Naturally occurring inhibitors regulate metabolism
- • Irreversible inhibition occurs when the inhibitordestroys the enzyme’s ability to interact with itsnormal substrate
inhibitor binds reversibly to an enzyme’sactive site, it competes with the substrate for thebinding site
noncompetitive inhibitor?or negative allosteric regulator
inhibitor binds reversibly to a site distinctfrom the active site, they act by changing the shape of the enzyme in sucha way that the active site can no longer bind thesubstrate
Allosteric regulators can stabilize the inactive form, but they can also....
stabilizethe active form (positive allosteric regulator)
What happends when a multi-subunit enzyme is allosterically regulated?
enzyme activation or inhibition occursvery quickly, like in a switch. The enzymebecomes very sensitive to regulator concentration
Cooperative allosteric transition?
occurs with two or more subunits
Positive allosteric regulation?
- transfer electrons.
- • A gain of electrons or hydrogen atoms is calledreduction.
- • The loss of electrons or hydrogen atoms is calledoxidation.
- • Whenever one material is reduced, another isoxidized.
Two metabolic processes are used in thebreakdown of glucose for energy?
- Glycolysis followed by cellular respiration
- Glycolysis followed by fermentation
About half of the energy from glucose is collected inATP (endergonic or exergonic?).
Oxidation of organicmolecules_______ the number of C-H bonds?
The cofactor _______is an essential electron carrierin cellular redox reactions?
Tendency to lose or gain electrons is called?
The oxidation of NADH with O2 as e- acceptor is?
- NADH + H+ + 1/2 O2 → NAD+ + H2O
- Two half reactions or redox pairs:
- NADH NAD+ ><+ H+ + 2e- (oxidation)
- 1/2 O2 + 2H+ ><+ 2e- H2O (reduction)
With O2 present, four major pathways operate?
- Pyruvate oxidation
- The citric acid cycle
- The respiratory chain (electron transport chain)
When no O2 is available, glycolysis is followed by?
Glycolysis can be divided into two stages?
- Investment of ATP to activate the sugarfollowed by splitting of C6 into 2x C3
- Oxidation of C3 giving NADH + H+ and ATPfollowed by recovery of initial ATPinvestment
The energy-harvesting reactions of glycolysis?
- The first reaction (a redox reaction) makes oneNADH + H+ per G3P molecule, and releasesenough energy to be coupled to the formationof an energy-rich P-bond per G3P.
- Two other reactions each yield one ATP perG3P molecule. This part of the pathway iscalled substrate-level phosphorylation.
- The final product is two 3-carbon molecules ofpyruvate.
Pyruvate is oxidized to acetate which is convertedto_______, which is fed into the citric acidcycle.
Pyruvate oxidation is a multistep reactioncatalyzed by an enzyme complex (60 subunits) in the__________.
The acetyl group is added to coenzyme A to form acetyl CoA. One__________ is generated duringthis reaction.
NADH + H+
Where does glyclysis happen?
How can an unfavorable reactions (positive ΔG°) be directly coupled to favorable ones (hydrolysis of ATP) or indirectly?
Energy Harvesting steps result in?
Pyruvate oxidation happends where? and what does it result in?
In mitochondria and results in Acetyl CoA
Certain redox potential corresponds to certain ΔG?
Glycolysis (cytoplasm): energy-investing steps, which occur because?
because ofcoupling to ATP hydrolysis or because of sequential coupling(last step with large -ΔG)Energy-harvesting steps
Citric acid cycle (inside mitochondria)?
completes the oxidation ofsugars to CO2 with help of dehydrogenases, results in reducedelectron carriers (NADH + H+ and FADH2)